Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010218.1 Corchorus capsularis cultivar CVL-1 contig10239, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 48274
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:361 original size:199 final size:198

Alignment explanation


    Indices: 9--663  Score: 854
    Period size: 199  Copynumber: 3.3  Consensus size: 198

          1 CCCACTTT

                   *          *       *                   *                  
          9 TGGAGTCCAAAATTTACAGTGACAGTTTATTGTATAATAATCCTATGAGAAAAAATT-TACTATA
          1 TGGAGTCTAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAG-AAAAATTATACTATA

                         *                  *                                
         73 -ACCGTAAGTGGAGTTTAGCAGACTGCACGTGTAGGGTTTAAGGGTTGACATGTGTCCCCTTAGG
         65 CACCGTAAGTGGAATTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGT-CCCTTAGG

                             **             *        *                  *    
        137 GAATATGTATTAATATTGTATATTTAATTGATGATGAAATGAGATATGTGTCAACTTCTTTACCC
        129 GAATATGTATTAATATTAAATATTTAATTGATTATGAAATGGGATATGTGTCAACTTCTTAACCC

                 
        202 GCTTA
        194 GCTTA

             *                       *  *      *         *                   
        207 TAGAGTCTAAAATTTACACTGACAGCGTGTTGTATGATAATCCTACAAGAAAAATTATA-TAATA
          1 TGGAGTCTAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACT-ATA

                         *              *    *                  *            
        271 CACCGTAAGTGGATTTTAGCAGACTGCAGGTGCGGGGTTTAAGGGTTGACATATGTCCCATTAGG
         65 CACCGTAAGTGGAATTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCC-TTAGG

                            *            *              *   *                
        336 GAATATGTATTAATATAAAATATTTAATTAATTATGAAATGGGGGTATATGTCAACTTCTTAACC
        129 GAATATGTATTAATATTAAATATTTAATTGATTATGAAAT-GGGATATGTGTCAACTTCTTAACC

                  
        401 CGCTTA
        193 CGCTTA

                               *        *              *                     
        407 TGGAGT-TCAAAATTTACATTGACAGTGGATTGTATAATAATCTTATAAGAAAAATTATACTATA
          1 TGGAGTCT-AAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATA

                       *              *                                  * **
        471 CACCGTCAA-TCGAATTTAGCAGACTACACGTGCAGGGTTTAAGGGTTGACATGTGTCCCTCAAT
         65 CACCGT-AAGTGGAATTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCTTAGG

                                                               *             
        535 GAATATGTATTAATATTAAATATTTAATTGATTATGAAATGGGATATGTGTTAACTTCTTAACCC
        129 GAATATGTATTAATATTAAATATTTAATTGATTATGAAATGGGATATGTGTCAACTTCTTAACCC

                 
        600 GCTTA
        194 GCTTA

                 * *                *                *                  
        605 -GGAAATGTAAAATTTACACTGAAAAGTGTATTGTATAATAGTCCTATAAGAAAAATTAT
          1 TGG-AGTCTAAAATTTACACTG-ACAGTGTATTGTATAATAATCCTATAAGAAAAATTAT

        664 GTAATGTGAT


Statistics
Matches: 395,  Mismatches: 51, Indels: 21
        0.85            0.11        0.04

Matches are distributed among these distances:
 197   10  0.03
 198   89  0.23
 199  165  0.42
 200  128  0.32
 201    3  0.01

ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34


Consensus pattern (198 bp):   
TGGAGTCTAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATAC
ACCGTAAGTGGAATTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCTTAGGGA
ATATGTATTAATATTAAATATTTAATTGATTATGAAATGGGATATGTGTCAACTTCTTAACCCGC
TTA

Found at i:3037 original size:8 final size:8

Alignment explanation


    Indices: 3024--3062  Score: 53
    Period size: 8  Copynumber: 5.0  Consensus size: 8

       3014 TTGGAAGAAG

                    
       3024 TAATATAA
          1 TAATATAA

                    
       3032 TAATATAA
          1 TAATATAA

                    
       3040 TAATA-AA
          1 TAATATAA

             *   *  
       3047 TGATAAAA
          1 TAATATAA

                    
       3055 TAATATAA
          1 TAATATAA

       3063 AGGCGGTAGA


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
   7    6  0.22
   8   21  0.78

ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33


Consensus pattern (8 bp):   
TAATATAA

Found at i:3058 original size:15 final size:16

Alignment explanation


    Indices: 3024--3062  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

       3014 TTGGAAGAAG

                         *  
       3024 TAATATAATAATATAA
          1 TAATATAATAATAAAA

                     *      
       3040 TAATA-AATGATAAAA
          1 TAATATAATAATAAAA

                    
       3055 TAATATAA
          1 TAATATAA

       3063 AGGCGGTAGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  15   13  0.65
  16    7  0.35

ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33


Consensus pattern (16 bp):   
TAATATAATAATAAAA

Found at i:18173 original size:17 final size:17

Alignment explanation


    Indices: 18153--18186  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      18143 TTGGGCCTAT

                       *     
      18153 TTGGAAATTGGCTTTGG
          1 TTGGAAATTGGATTTGG

                *            
      18170 TTGGTAATTGGATTTGG
          1 TTGGAAATTGGATTTGG

      18187 AATGGACAAT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.18, C:0.03, G:0.35, T:0.44


Consensus pattern (17 bp):   
TTGGAAATTGGATTTGG
Done.